Category Archives: howto

Video Tutorial: editing R plots in Adobe Illustrator

Adobe Illustrator is a powerful tool for creating and editing figures; unfortunately, it’s also really intimidating. So today at The Molecular Ecologist we’re trying something a little different: a screen-capture video tutorial about using Adobe Illustrator to enhance and edit plots … Continue reading

Posted in howto, R | Tagged , , , , , , , , | 3 Comments

On (mis)interpreting STRUCTURE/ADMIXTURE results

STRUCTURE, ADMIXTURE and other similar software are among the most cited programs in modern population genomics. They are algorithms that estimate allele frequencies and admixture proportions under the premise that sampled genotypes are derived from one of “K” ancestral populations, … Continue reading

Posted in bioinformatics, genomics, howto, methods, population genetics, software, STRUCTURE | Tagged , , , , | 1 Comment

Making Maps in R, volume 2: ggplots

The open-source statisical programming environment R is truly a Swiss Army knife for molecular ecology. With the right code, R can processes genetic data and trait measurements, analyze how genetic variants relate to traits, reconstruct phylogenetic trees, and illustrate the … Continue reading

Posted in howto, R, software | Tagged , | 7 Comments

10 simple rules for designing a scientific poster

Conference season is upon us! Around the world, thousands of scientists face a daunting task: designing a scientific poster. It should be sleek, yet informative; eye-catching, yet professional; and most of all it should attract the attention of your future … Continue reading

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How to make the most out of your phylogenetic study

Phylogenetic studies are crucial for ecology and evolution. However, their usefulness for comparative biology or meta-analyses can vary considerably. Especially the inclusion of unidentified species (“Balanus sp.”) obstructs their use in comparative studies. How can I attach life history or morphological data … Continue reading

Posted in data archiving, evolution, howto, phylogenetics, Uncategorized | Leave a comment

Using R to mine species data

Many of us generate more data than we know what to do with (speaking of which: keep an eye out for the 2016 NGS Field Guide, coming soon!), so it’s easy to forget about the piles of data already at our fingertips. Research potential is … Continue reading

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The 2016 Next-Generation Sequencing Field Guide Preview: Zombie Systems and New Hope

After a year of minimal activity, we finally have some significant changes in Next Gen Land. In the 2016 update of the NGS Field Guide, I will continue to give my overall interpretation about the various instruments, but with less … Continue reading

Posted in genomics, howto, methods, RNAseq, transcriptomics | Tagged , , , | 8 Comments

Geographical Heat Maps in R

I go crazy for fancy data visualizations in R, and a figure in a recent publication has had me wondering if there is an easy way to incorporate density distributions (or as in their case, a distribution of f4 statistics, … Continue reading

Posted in bioinformatics, howto, R, software | Tagged , | 2 Comments

Quick and dirty tree building in R

One of the major obstacles to turning your sequence data into phylogenetic trees is choosing (and learning) a tree-building program. Confounding this problem is the fact that most researchers will want to perform numerous, complementary analyses, each of which may … Continue reading

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2D Posterior Density Plots in R

I have been grappling with visualizing two dimensional histograms of posterior density distributions of parameters, as estimated by one of your favorite programs – IMa2, MIGRATE-n, MSVAR, etc. All these programs print out distributions of estimated parameters, and here’s a … Continue reading

Posted in bioinformatics, howto, population genetics, R, software | Tagged , , , | 1 Comment